Torrential rain meant just 8559 turned up to watch the Brumbies' season end with a controversial loss to the Otago Highlanders at Canberra Stadium on Friday night.

As hosts of the qualifying final they have to pay the Highlanders a set amount and then they get whatever is left over after other costs, including stadium hire, are taken care of.

Thomson said they wouldn't know the final figures for a few days, but breaking even was looking like the best possible outcome.

They'd sold more than 10,000 tickets, but the weather kept a lot of people away and ruined hopes of getting 15,000 there.

"We won't know the final figure for a couple of days into the week. We have to work out a number of things, stadium costs and all that sort of stuff, but at the moment we'd be hoping to break even at best," Thomson said on Sunday.

"We can't do anything about the weather. It's certainly disappointing, we would have loved to have 12-15,000 people there if it was a nice night.

"Hats off to all the people that ended up coming out to the game, because the weather was pretty atrocious all through Friday ... it was a great effort just to get that amount there."

The Brumbies went into this financial year hoping to record a $1 million profit, but a payout to former boss Michael Jones and several other factors means they'll post another loss this year.

It would be the Brumbies' sixth consecutive loss, during which time their cash reserves from the $11.375 million sale of their Griffith base have been almost completely whittled away.

The Brumbies have struggled to turn around declining crowds, with an average of just 9259 for their last three home games of the season.

Thomson felt Canberra's cold July weather and some poor-quality opposition – the Queensland Reds and Western Force both finished in the bottom four – were to blame. Crowds had been good until then.

Despite the Brumbies' financial woes, he was confident the two-time Super Rugby champions still had a future.

"There's no doubt about the future of the Brumbies in Canberra," Thomson said.

"At the front of the season our crowds were very good and our crowds were up on last year and we were tracking really well."

The Brumbies asked for all of this year's home games to be afternoon games to try to avoid Canberra's cold, but Super Rugby's governing body SANZAAR only gave them one – against the Canterbury Crusaders in April.

Thomson said they would continue to push for as many afternoon games as possible.

"Our request for this time of year and our preference would be for afternoon games, but we understand the TV ratings through Fox are important to the financial side of things for the competition also," he said.

"We'll continue to push for [afternoon] time slots at this time of year, but we're in the hands of the broadcasters and SANZAAR."

He said the Brumbies board will begin advertising for a chief executive over the next "couple of weeks" and he expected to be replaced within the three-six-month period originally predicted.

Thomson said he wouldn't throw his hat in the ring and would return to his integrity manager role with the Australian Rugby Union.